Hox genes encode transcription factors essential for patterning the anterior to posterior animal body axis. In vertebrates, these genes are arranged in clusters. During development, Hox genes are activated in a time sequence that follows their physical order within the cluster. To elucidate the mechanism of ‘temporal collinearity’ we looked at the in vivo dynamics of chromatin state during successive Hox gene activation in the mouse embryo. We show that chromatin marks are important parameters in the temporal regulation of the Hox gene family as judged by the dynamic progression of transcription-competent modifications: increases in activation marks correspond to decreases in repressive marks. Furthermore, using a mouse where a Hox cluster was split into two pieces, we document the necessity to maintain a clustered organization to properly implement this temporal process.